[phenixbb] Hinge movement for refine?

Pavel Afonine pafonine at lbl.gov
Thu Oct 4 14:07:18 PDT 2007


Hi Partha,

here is an example of slightly more complex selections:
refinement.refine.sites {
  rigid_body = chain A and (resid 2:135 or resid 410:525)
  rigid_body = chain A and (resid 136:194 or resid 375:409)
  rigid_body = chain A and (resid 195:374)
  rigid_body = chain B and (resid 2:135 or resid 410:525)
  rigid_body = chain B and (resid 136:194 or resid 375:409)
  rigid_body = chain B and (resid 195:374)
  rigid_body = chain C and (resid 2:135 or resid 410:525)
  rigid_body = chain C and (resid 136:194 or resid 375:409)
  rigid_body = chain C and (resid 195:374)
}

see also phenix.refine Manual (Atom selection examples):
http://phenix-online.org/documentation/refinement.htm

Pavel.


Partha Chakrabarti wrote:
> Hiya,
> I have used rigid body refinement in phenix.refine as suggested:
>
> refinement.refine.sites {
>   rigid_body = chain A
>   rigid_body = chain B
> }
>
> If I have a multidomain protein like kinases, or G proteins which have 
> flexible switches, how can I define the region within a given chain?
>
> Best, Partha
>
> -- 
> MRC National Institute for Medical Research
> Division of Molecular Structure
> The Ridgeway, NW7 1AA, UK
> Email: pchakra at nimr.mrc.ac.uk <mailto:pchakra at nimr.mrc.ac.uk>
> Phone: + 44 208 816 2515
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